Ghana's president John Dramani Mahama described the loss of life as "catastrophic and almost unprecedented", as he toured the scene of the disaster on Thursday morning.
A fire brigade spokesman said many of the victims had sought shelter there from torrential rain which has flooded the city.
Communications minister Edward Omane Boamah described the situation as a "national emergency".
It was not immediately clear exactly how the victims died, with reports that some had drowned in flood waters caused by blocked roadside gutters and drains that overflowed because of the rains.
Local hospitals said morgues were full, with the death toll likely to rise, according to security officials.
The blast was caused by a fire that erupted in a nearby lorry terminal at around 10:00pm (local time) on Wednesday then spread to the gas station and other buildings in Accra, Prince Billy Anaglate told a local radio station.
Initial signs suggested the fire started by accident, he added.
Firefighters battled the blaze into the early hours while police and soldiers joined emergency crews helping rescue people trapped in the wreckage, said city mayor Oko Vanderpuije.
At least two days of rains have caused chaos in Accra, leaving many suburbs submerged and people stranded.
Already sketchy power supplies had been cut to some communities as electricity sub-stations were submerged.
Mr Boamah said the armed forces, police, fire and the National Disaster Management Organisation have been deployed to help those affected.
"The general public is kindly advised to avoid fast-moving rainwater and areas they know have big drains. Stay on higher ground, where necessary, to prevent loss of life," he said.
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